So that is just a "false floor" in the storage area, correct?
Are there any drains?
I suspect it's a very simple false floor and not sealed in any way so water that gets in there will pass right through cracks around the edge and into the bilge? Pour some water in there and see what happens.
I see the waterline you're talking about - that could have been from a plug in the bilge drain system at some point or even the boat stored with the bow down and water was allowed to collect.
Options... replumb the drains to the forward bilge... replumb the drains directly through the false floor.